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McIlvin"],"software":[""],"tissue":["Permanent Cell Line Cell"],"sample_protocol":["P. aeruginosa strains MPAO1 and a cntM knockout strain were used. Cultures were grown in M9 minimal medium with or without the addition of 14.2 µM Zn2+. Protein extraction was performed based on the method described by Hughes et al. All reagents were prepared using Optima LC-MS grade water. Briefly, thawed cells were re-pelleted by centrifugation for 20 minutes at 14 100 x g in an ethanol-washed low adhesion 2 mL microcentrifuge tube (USA Scientific, part 1420-2600). 430 µL lysis buffer (50 mM HEPES pH 8.5 (Boston BioProducts/1% SDS (Fisher Scientific)) was added to the pellet, mixed, then 30 µL was withdrawn for protein quantification.  Cells were then treated with 50 units of benzonase nuclease (Novagen) to degrade chromatin and incubated at 37 ˚C for 40 minutes. The samples were incubated for 30 minutes at 45 ˚C with 20 µL of 200 mM dithiothreitol (DTT) (Fisher Bioreagents) in 50 mM HEPES pH 8.5 to reduce disulfide bonds, then for 30 minutes in the dark at 24˚C with 40 µL of 400 mM iodoacetamide (Acros Organics) in 500 mM HEPES pH 8.5 to alkylate sulfhydryl groups. The iodoacetamide reaction was quenched with 40 µL of the DTT solution. Protein clean-up was then performed using a mixed magnetic bead solution of 0.70-1.10 µm and 1 µm average particle size (GE Healthcare UK Limited). 400 ug magnetic beads were added per 400 µL lysate. The solution was acidified to pH 2 using formic acid, then protein binding to the beads was induced with the addition of 1100 µL of 100% acetonitrile. The samples were then incubated at 37 ˚C in an Eppendorf Thermomixer R for 15 minutes, followed by 30 minutes at room temperature and 2 minutes on a magnetic rack. After removing the supernatant, samples were washed with 1400 µL of 70% ethanol followed by 1400 µL of 100% acetonitrile. The beads were then dried until the acetonitrile evaporated and reconstituted in 90 µL of 50 mM HEPES pH 8. The beads were incubated at room temperature for two hours. Proteins were quantified using a Micro BCA protein assay kit (Thermo Scientific) and a Nanodrop ND-1000 Spectrophotometer. A bovine serum albumin standard (Thermo Scientific) was used to create a standard curve (R2=0.997). Trypsin (Promega, V5280) was added in a ratio of 1:20 trypsin to protein, then samples were incubated at 37 ˚C for 20 hours. The digested samples were then washed using a final concentration of 95% acetonitrile then with 100% acetonitrile, then subsequently air-dried. The dried beads were reconstituted in 2% DMSO for a final protein concentration of 1.1 µg/µL. Following a 15-minute incubation of a magnetic rack, the supernatant was transferred to a clean tube, then again transferred after a 5-minute incubation. 1% formic acid was then added to a final concentration of 0.1% and a 1 µg/µL protein concentration. Samples were then frozen at -20 ˚C until analysis. The samples were analyzed using liquid chromatography tandem mass spectrometry (LC/MS/MS) with a Michrom Advance HPLC reverse phase chromatography system paired with a Thermo Scientific Q-Exactive Orbitrap mass spectrometer using a Michrom Advance CaptiveSpray source. Before injection, samples were concentrated onto a C18 trap column, rinsed with 100 µL of a 0.1% formic acid, 2% acetonitrile (ACN) and 97.9% water solution before gradient elution with a reverse phase C18 column using a 500 nL/min flow rate. All solvents were prepared with Fisher Optima grade reagents. Liquid chromatography was a nonlinear 240-minute gradient from 5% to 95% buffer B, where A was 0.1% formic acid in water and B was 0.1% formic acid in ACN. Two modes of mass spectrometry were used to acquire data. Biological triplicates were used for DDA analysis. For DIA analysis, biological triplicates were used for MPAO1 treatments and duplicates for ∆cntM treatments. During DDA analysis, MS1 scans proceeded from 380 m/z to 1280 m/z using a 70K resolution. The top 10 ions underwent MS2 scans with a 2.0 m/z isolation window and a 15 second dynamic exclusion time. During DIA analysis, the MS1 scan range was 285 m/z to 1015 m/z with a 60K resolution. The DIA scans comprised a precursor range of 400 m/z to 1000 m/z with 25 non-overlapping windows of 24 m/z. The MS2 resolution was 30K."],"repository":["Pride"],"labhead":["Mak Saito"],"instrument_platform":[""],"submission_type":["COMPLETE"],"labhead_affiliation":["Marine Chemistry and Geochemistry Woods Hole Oceanographic Institution"],"publication":["40580114 Meyer ACS, McIlvin MR, Lopez P, Searle BC, Saito MA. Proteomic profiling of zinc homeostasis mechanisms in Pseudomonas aeruginosa through data-dependent and data-independent acquisition mass spectrometry. Metallomics. 2025 17(8):mfaf020 10.1093/mtomcs/mfaf020"],"submitter_affiliation":["Woods Hole Oceanographic Inst."],"labhead_mail":["msaito@whoi.edu"],"technology_type":["Mass Spectrometry","Shotgun proteomics","SWATH MS"],"disease":["Disease Free"],"submitter_keywords":["Pseudopaline","Lc-msms","Metalloprotein","Abc transporter","Biofilm","Pseudomonas aeruginosa","Zinc"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD047454"],"quantification_method":[""],"modification":[""],"data_protocol":["The generated mass spectra from DDA analysis were searched against the P. aeruginosa translated genome using the SEQUEST HT algorithm within Proteome Discoverer 2.2 (Thermo Scientific). We used a fragment tolerance of 0.02 Da, a parent tolerance of 10.0 ppm, and a +57 carbamidomethyl fixed modification on cysteine. Variable modifications were a +16 oxidation modification on methionine and a +42 acetyl modification on the N-terminus. A maximum of two missed cleavages were allowed. Identification thresholds were 95.0% for peptides and 99.0% for proteins (minimum two peptides), giving a protein false discovery rate of 0.4% using decoys generated from a reverse database. Annotation and processing were performed using Scaffold 5.0.1 (Proteome Software, Portland, Oregon, USA).   The spectra from DIA analysis were processed using several tools within ScaffoldDIA (Proteome Software, Portland, Oregon, USA). First, staggered windows were deconvoluted using ProteoWizard (3.0.11748).  Spectra were searched against the P. aeruginosa translated genome using a 10.0 ppm peptide mass tolerance and a 10.0 ppm fragment mass tolerance, and only peptides of length 6 to 30 and charge 2 to 3 were included. A maximum of 1 missed cleavage was permitted. False discovery rates were calculated using decoys generated from a reverse database. Percolator (3.01.nightly-13.655e4c5-dirty) was used to filter peptides in each sample to achieve a maximum false discovery rate of 0.01, then individual search results were combined and posterior error probabilities were generated for all peptide spectral matches. These results were filtered to a false discovery rate threshold by Percolator. EncylopeDIA (1.12.31) was used to quantify peptides using the 5 fragment ions of highest quality. Protein groups were created if peptides corresponded well to more than one protein. Protein identifications were filtered to a threshold false discovery rate of <1.0%. Log2 fold-change values were calculated from normalized exclusive intensities."],"omics_type":["Proteomics"],"species":["Pseudomonas Aeruginosa Pao1"],"submitter_mail":["mmcilvin@whoi.edu"],"submitter_country":["United States"],"doi":["10.6019/PXD047454"],"pubmed_abstract":["Zinc is central to the function of many proteins, yet the mechanisms of zinc homeostasis and their interplay with other cellular systems remain underexplored. In this study, we employ data-dependent acquisition (DDA) and data-independent acquisition (DIA) mass spectrometry to investigate proteome changes in Pseudomonas aeruginosa under conditions of different zinc availability. Using both methods, we detected a combined 2143 unique proteins, 1578 of which were identified by both DDA and DIA. We demonstrated that most of the previously described Zn homeostasis systems exhibit proteomic responses that follow similar trends to those seen in transcriptomics studies. Furthermore, changes in abundance of multiple Zn-metalloproteins and Zn-independent homologs were clearly observable, with respective increases and decreases when Zn was provided, though the magnitude of these changes varied. Most of the Zn-metalloproteins observed were located in one of two Zur-regulated operons between PA5534 and PA5541. This study provides a view of Zn homeostasis mechanisms that is complementary to existing transcriptomics investigations: as gene transcripts are not strictly proportional to the actual distribution of proteins within a cell, analysis of the proteome offers another way to assess the relative use and importance of similar or ostensibly redundant systems in different conditions and can highlight shifts in metal prioritization between metalloproteins."],"pubmed_title":["Proteomic profiling of zinc homeostasis mechanisms in Pseudomonas aeruginosa through data-dependent and data-independent acquisition mass spectrometry."],"pubmed_authors":["Meyer Annaliese C S ACS, McIlvin Matthew R MR, Lopez Paloma P, Searle Brian C BC, Saito Mak A MA"],"additional_accession":[]},"is_claimable":false,"name":"A proteomic perspective on homeostasis mechanisms and broader cellular effects of zinc on model prokaryote Pseudomonas aeruginosa","description":"Zinc is central to the function of many proteins, yet the mechanisms of zinc homeostasis and its impact on other cellular regulatory systems remain under-characterized. In this study, we used the opportunistic human pathogen and environmentally significant model organism Pseudomonas aeruginosa to explore zinc activity via proteomic methods. Overall, we identified 2120 proteins using data-dependent acquisition mass spectrometry and 1909 proteins using data-independent acquisition mass spectrometry, 1667 of which were shared between the two methods. We showed that ATP-binding cassette (ABC) transporters are significant methods of zinc uptake in this system via upregulation of associated proteins when P. aeruginosa was grown under low zinc conditions. Previously identified zinc efflux mechanisms, such as P-type ATPase transporter ZntA and resistance-nodulation-cell division cation efflux transporter CzcA responded to high zinc conditions, emphasizing the importance of tight regulation of intracellular zinc in both depleted and replete habitats. Protein associated with biofilm formation was impacted by the presence of zinc and the ability of the strains used to produce pseudopaline, a biogenic zinc-complexing molecule. Pseudopaline-deficient strains, which lacked the CntM synthesis protein, contained more abundant protein biomarkers for the formation of mature biofilms. We speculate that a previously undescribed system exists in which pseudopaline complexation of extracellular zinc provides a protection from free zinc ions. In the absence of this compound, zinc ions induce a RsmA-GacS/A mediated response that promotes the transition to a biofilm lifestyle.","dates":{"publication":"2026-08-31","submission":"2023-12-01"},"accession":"PXD047454","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:35795","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:57577","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:1073882","NEWT:6819","NEWT:112509","NEWT:475174","NEWT:111205","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:12215","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:4615","NEWT:67352","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:3760","NEWT:1584","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:29064","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:273791","NEWT:3347","NEWT:49928","NEWT:3349","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:55350","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:345076","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:171719","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:260499","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:717966","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:34878","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:45972","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:2836","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1579","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:321967","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:191701","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:11723","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:906914","NEWT:81231006","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:548","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:872227","NEWT:13076","NEWT:2587410","NEWT:207340","NEWT:172271","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:2126337","NEWT:550","NEWT:33941","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:9995","NEWT:575412","NEWT:28112","NEWT:49012","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:64657","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT: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